Starting phenix.real_space_refine on Sun Jul 5 17:51:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.map" model { file = "/net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vau_31864/07_2026/7vau_31864.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18720 2.51 5 N 5125 2.21 5 O 5558 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29513 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 577, 4466 Classifications: {'peptide': 577} Link IDs: {'PTRANS': 35, 'TRANS': 541} Chain breaks: 1 Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.70, per 1000 atoms: 0.23 Number of scatterers: 29513 At special positions: 0 Unit cell: (137.28, 178.64, 153.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 5 15.00 Mg 2 11.99 O 5558 8.00 N 5125 7.00 C 18720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.71 Conformation dependent library (CDL) restraints added in 1.3 seconds 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6916 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 26 sheets defined 47.0% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 90 through 98 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 245 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.811A pdb=" N MET A 262 " --> pdb=" O ARG A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 297 through 316 removed outlier: 4.410A pdb=" N ALA A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 342 removed outlier: 3.977A pdb=" N TRP A 330 " --> pdb=" O SER A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 393 through 401 removed outlier: 3.613A pdb=" N ARG A 401 " --> pdb=" O GLN A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 432 through 434 No H-bonds generated for 'chain 'A' and resid 432 through 434' Processing helix chain 'A' and resid 435 through 443 Processing helix chain 'A' and resid 446 through 472 removed outlier: 4.124A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.718A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 535 through 540 removed outlier: 3.646A pdb=" N ILE A 539 " --> pdb=" O SER A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.796A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 554 No H-bonds generated for 'chain 'A' and resid 552 through 554' Processing helix chain 'A' and resid 555 through 557 No H-bonds generated for 'chain 'A' and resid 555 through 557' Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.604A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.826A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.507A pdb=" N LEU B 341 " --> pdb=" O ILE B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 353 through 364 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.708A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 464 removed outlier: 3.641A pdb=" N LEU B 464 " --> pdb=" O ARG B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.524A pdb=" N GLN B 469 " --> pdb=" O GLN B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 476 Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 533 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.346A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 Processing helix chain 'B' and resid 558 through 573 removed outlier: 3.604A pdb=" N TYR B 562 " --> pdb=" O GLU B 558 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 577 Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 245 Processing helix chain 'C' and resid 259 through 269 Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 4.355A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 342 removed outlier: 4.173A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 removed outlier: 3.512A pdb=" N ASP C 390 " --> pdb=" O PRO C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 393 through 400 Processing helix chain 'C' and resid 410 through 416 removed outlier: 3.510A pdb=" N ALA C 414 " --> pdb=" O ASP C 410 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG C 416 " --> pdb=" O SER C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 4.336A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 471 " --> pdb=" O ILE C 467 " (cutoff:3.500A) Processing helix chain 'C' and resid 473 through 476 Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 533 Processing helix chain 'C' and resid 535 through 541 Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.847A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 578 removed outlier: 3.802A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS C 575 " --> pdb=" O GLN C 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.574A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 removed outlier: 3.673A pdb=" N SER D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 179 " --> pdb=" O PRO D 175 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 174 through 179' Processing helix chain 'D' and resid 197 through 211 removed outlier: 3.891A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 removed outlier: 3.811A pdb=" N TYR D 263 " --> pdb=" O ASP D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.813A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 422 Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'E' and resid 85 through 89 removed outlier: 3.823A pdb=" N LEU E 89 " --> pdb=" O LYS E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 removed outlier: 3.562A pdb=" N ILE E 163 " --> pdb=" O PRO E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 removed outlier: 4.018A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 211 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 228 through 232 Processing helix chain 'E' and resid 233 through 250 Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.642A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.641A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 333 removed outlier: 3.694A pdb=" N ILE E 332 " --> pdb=" O LEU E 328 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.799A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 3.892A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 457 through 462 removed outlier: 4.005A pdb=" N LYS E 461 " --> pdb=" O ASP E 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.747A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.585A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 removed outlier: 3.533A pdb=" N SER F 178 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.690A pdb=" N GLU F 230 " --> pdb=" O PRO F 227 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG F 231 " --> pdb=" O THR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.536A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.661A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 removed outlier: 3.530A pdb=" N LYS F 346 " --> pdb=" O GLU F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 365 removed outlier: 3.532A pdb=" N ASN F 364 " --> pdb=" O LEU F 361 " (cutoff:3.500A) Processing helix chain 'F' and resid 374 through 399 Processing helix chain 'F' and resid 400 through 404 removed outlier: 3.729A pdb=" N ALA F 403 " --> pdb=" O GLY F 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 470 Processing helix chain 'G' and resid 7 through 71 removed outlier: 3.696A pdb=" N ARG G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 83 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.597A pdb=" N ALA G 112 " --> pdb=" O PRO G 109 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU G 113 " --> pdb=" O ASP G 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 109 through 113' Processing helix chain 'G' and resid 120 through 167 removed outlier: 3.813A pdb=" N GLU G 125 " --> pdb=" O ALA G 121 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 209 Processing helix chain 'H' and resid 6 through 16 removed outlier: 4.223A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 39 Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.717A pdb=" N ALA H 58 " --> pdb=" O ASP H 54 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N VAL H 59 " --> pdb=" O PRO H 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 54 through 59' Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.714A pdb=" N PHE H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 106 removed outlier: 3.840A pdb=" N GLU I 90 " --> pdb=" O ALA I 86 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA I 105 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ARG I 106 " --> pdb=" O LYS I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 Processing helix chain 'J' and resid 62 through 93 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.866A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 128 through 133 Processing helix chain 'J' and resid 170 through 187 removed outlier: 4.119A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N SER J 180 " --> pdb=" O ASP J 176 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N LYS J 181 " --> pdb=" O ALA J 177 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 119 removed outlier: 3.771A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG K 106 " --> pdb=" O LYS K 102 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP K 108 " --> pdb=" O MET K 104 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU K 109 " --> pdb=" O ALA K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 93 Processing helix chain 'L' and resid 94 through 97 Processing helix chain 'L' and resid 99 through 115 Processing helix chain 'L' and resid 131 through 139 removed outlier: 3.652A pdb=" N ALA L 135 " --> pdb=" O LEU L 131 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG L 136 " --> pdb=" O GLU L 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 187 removed outlier: 4.537A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.516A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.783A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 5.995A pdb=" N ILE B 39 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLN B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 41 " --> pdb=" O PHE B 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.565A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP C 43 " --> pdb=" O THR C 46 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 5.787A pdb=" N VAL D 47 " --> pdb=" O GLN D 58 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N GLN D 58 " --> pdb=" O VAL D 47 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLU D 49 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N TYR D 54 " --> pdb=" O SER D 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 22 current: chain 'E' and resid 45 through 51 removed outlier: 5.893A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR E 54 " --> pdb=" O SER E 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 54 through 59 current: chain 'F' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 22 current: chain 'F' and resid 45 through 51 removed outlier: 5.814A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR F 54 " --> pdb=" O SER F 51 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 54 through 59 current: chain 'J' and resid 162 through 167 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 162 through 167 current: chain 'L' and resid 151 through 155 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 143 through 148 removed outlier: 3.828A pdb=" N GLU A 140 " --> pdb=" O PHE A 143 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N ALA A 118 " --> pdb=" O PRO A 139 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 7.057A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA7, first strand: chain 'B' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 82 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 383 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 120 through 121 removed outlier: 3.893A pdb=" N GLY B 136 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 128 through 129 removed outlier: 6.814A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 405 through 406 Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 291 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 148 removed outlier: 3.894A pdb=" N GLY C 136 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY C 164 " --> pdb=" O TRP C 119 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 6.788A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 173 " --> pdb=" O LEU C 181 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 93 Processing sheet with id=AB8, first strand: chain 'E' and resid 92 through 94 removed outlier: 7.013A pdb=" N VAL E 189 " --> pdb=" O VAL E 218 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N PHE E 220 " --> pdb=" O VAL E 189 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N PHE E 191 " --> pdb=" O PHE E 220 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA E 188 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N ILE E 256 " --> pdb=" O ALA E 188 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N VAL E 190 " --> pdb=" O ILE E 256 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.679A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 313 through 315 removed outlier: 5.604A pdb=" N GLN E 338 " --> pdb=" O PRO E 356 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 81 through 84 removed outlier: 3.590A pdb=" N LYS F 110 " --> pdb=" O VAL F 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.527A pdb=" N PHE F 93 " --> pdb=" O LEU F 221 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL F 189 " --> pdb=" O VAL F 218 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N PHE F 220 " --> pdb=" O VAL F 189 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHE F 191 " --> pdb=" O PHE F 220 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL F 253 " --> pdb=" O THR F 309 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ILE F 311 " --> pdb=" O VAL F 253 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL F 255 " --> pdb=" O ILE F 311 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ILE F 313 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU F 257 " --> pdb=" O ILE F 313 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N SER F 315 " --> pdb=" O LEU F 257 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 144 through 145 removed outlier: 4.552A pdb=" N LEU F 144 " --> pdb=" O ILE F 131 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 278 through 280 removed outlier: 6.448A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 93 through 96 Processing sheet with id=AC7, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.000A pdb=" N VAL H 3 " --> pdb=" O TYR H 21 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL H 45 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 120 through 123 removed outlier: 6.174A pdb=" N LEU J 121 " --> pdb=" O LEU J 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 1291 hydrogen bonds defined for protein. 3705 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.42 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9328 1.33 - 1.45: 3589 1.45 - 1.57: 16948 1.57 - 1.69: 8 1.69 - 1.81: 194 Bond restraints: 30067 Sorted by residual: bond pdb=" C4 ADP A 601 " pdb=" C5 ADP A 601 " ideal model delta sigma weight residual 1.490 1.384 0.106 2.00e-02 2.50e+03 2.81e+01 bond pdb=" C5 ADP A 601 " pdb=" C6 ADP A 601 " ideal model delta sigma weight residual 1.490 1.408 0.082 2.00e-02 2.50e+03 1.69e+01 bond pdb=" O3B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.584 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C VAL B 123 " pdb=" N LYS B 124 " ideal model delta sigma weight residual 1.327 1.371 -0.045 1.39e-02 5.18e+03 1.02e+01 bond pdb=" O2B ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 1.510 1.470 0.040 2.00e-02 2.50e+03 3.93e+00 ... (remaining 30062 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.17: 40534 3.17 - 6.34: 191 6.34 - 9.51: 13 9.51 - 12.68: 0 12.68 - 15.85: 2 Bond angle restraints: 40740 Sorted by residual: angle pdb=" PA ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " ideal model delta sigma weight residual 120.50 136.35 -15.85 3.00e+00 1.11e-01 2.79e+01 angle pdb=" O1B ADP A 601 " pdb=" PB ADP A 601 " pdb=" O3B ADP A 601 " ideal model delta sigma weight residual 119.90 107.17 12.73 3.00e+00 1.11e-01 1.80e+01 angle pdb=" C GLY B 256 " pdb=" N GLU B 257 " pdb=" CA GLU B 257 " ideal model delta sigma weight residual 121.91 113.61 8.30 2.03e+00 2.43e-01 1.67e+01 angle pdb=" N GLY B 256 " pdb=" CA GLY B 256 " pdb=" C GLY B 256 " ideal model delta sigma weight residual 113.18 104.76 8.42 2.37e+00 1.78e-01 1.26e+01 angle pdb=" CA GLU F 296 " pdb=" C GLU F 296 " pdb=" N ARG F 297 " ideal model delta sigma weight residual 118.27 123.19 -4.92 1.59e+00 3.96e-01 9.57e+00 ... (remaining 40735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.47: 17192 22.47 - 44.94: 982 44.94 - 67.41: 107 67.41 - 89.88: 29 89.88 - 112.35: 1 Dihedral angle restraints: 18311 sinusoidal: 7493 harmonic: 10818 Sorted by residual: dihedral pdb=" CA ALA J 169 " pdb=" C ALA J 169 " pdb=" N ARG J 170 " pdb=" CA ARG J 170 " ideal model delta harmonic sigma weight residual 180.00 151.11 28.89 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 -172.35 112.35 1 2.00e+01 2.50e-03 3.31e+01 dihedral pdb=" CA LEU J 168 " pdb=" C LEU J 168 " pdb=" N ALA J 169 " pdb=" CA ALA J 169 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 18308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2921 0.041 - 0.082: 1206 0.082 - 0.123: 386 0.123 - 0.164: 52 0.164 - 0.205: 2 Chirality restraints: 4567 Sorted by residual: chirality pdb=" CA PHE B 419 " pdb=" N PHE B 419 " pdb=" C PHE B 419 " pdb=" CB PHE B 419 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" C2' ADP A 601 " pdb=" C1' ADP A 601 " pdb=" C3' ADP A 601 " pdb=" O2' ADP A 601 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.16 2.00e-01 2.50e+01 6.78e-01 chirality pdb=" CA GLU D 296 " pdb=" N GLU D 296 " pdb=" C GLU D 296 " pdb=" CB GLU D 296 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.32e-01 ... (remaining 4564 not shown) Planarity restraints: 5329 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 393 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.02e+00 pdb=" N PRO A 394 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 394 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 394 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 228 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.88e+00 pdb=" N PRO B 229 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 229 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 229 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO E 324 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.022 5.00e-02 4.00e+02 ... (remaining 5326 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 170 2.55 - 3.14: 23255 3.14 - 3.73: 44504 3.73 - 4.31: 62372 4.31 - 4.90: 107258 Nonbonded interactions: 237559 Sorted by model distance: nonbonded pdb=" OG SER C 235 " pdb="MG MG C 602 " model vdw 1.966 2.170 nonbonded pdb=" O2G ATP C 601 " pdb="MG MG C 602 " model vdw 1.967 2.170 nonbonded pdb=" OG SER E 431 " pdb=" OE1 GLU E 434 " model vdw 2.129 3.040 nonbonded pdb=" OE1 GLU F 109 " pdb=" OH TYR F 244 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR D 263 " pdb=" OD2 ASP D 290 " model vdw 2.162 3.040 ... (remaining 237554 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 32 or resid 34 through 578)) selection = chain 'B' selection = (chain 'C' and (resid 1 through 32 or resid 34 through 578)) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.740 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.106 30068 Z= 0.316 Angle : 0.686 15.852 40740 Z= 0.362 Chirality : 0.048 0.205 4567 Planarity : 0.005 0.048 5329 Dihedral : 13.627 112.351 11395 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.14), residues: 3761 helix: 1.62 (0.13), residues: 1542 sheet: -0.18 (0.23), residues: 561 loop : -0.10 (0.15), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 364 TYR 0.025 0.002 TYR D 331 PHE 0.017 0.002 PHE D 418 TRP 0.012 0.002 TRP B 119 HIS 0.007 0.002 HIS D 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.32 (30067) covalent geometry : angle 0.68649 / 0.36 (40740) hydrogen bonds : bond 0.15462 / 10.48 ( 1291) hydrogen bonds : angle 6.20067 / 4.35 ( 3705) Misc. bond : bond 0.00020 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3710 (mtt) cc_final: 0.3285 (ptm) REVERT: A 20 LEU cc_start: 0.7378 (tp) cc_final: 0.7140 (tp) REVERT: A 29 LYS cc_start: 0.7892 (mmtp) cc_final: 0.7531 (mmmt) REVERT: A 54 ASP cc_start: 0.7649 (t0) cc_final: 0.7231 (t70) REVERT: A 158 LYS cc_start: 0.6661 (mtpt) cc_final: 0.6304 (mttt) REVERT: A 369 ILE cc_start: 0.8782 (mm) cc_final: 0.8438 (mm) REVERT: A 390 ASP cc_start: 0.7731 (t0) cc_final: 0.7519 (t70) REVERT: A 441 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6933 (mm-30) REVERT: A 532 ARG cc_start: 0.6222 (mtm-85) cc_final: 0.5752 (ttp80) REVERT: A 550 ARG cc_start: 0.6793 (tpp-160) cc_final: 0.6280 (mmt90) REVERT: A 556 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6834 (tp30) REVERT: A 568 LYS cc_start: 0.6730 (mtmt) cc_final: 0.6436 (tttt) REVERT: B 133 MET cc_start: 0.7343 (mtp) cc_final: 0.7067 (mtm) REVERT: B 143 PHE cc_start: 0.6081 (t80) cc_final: 0.5590 (m-80) REVERT: B 156 ARG cc_start: 0.6771 (ptm160) cc_final: 0.5999 (ptp90) REVERT: B 338 SER cc_start: 0.8193 (t) cc_final: 0.7735 (m) REVERT: B 342 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7575 (mt-10) REVERT: B 408 ARG cc_start: 0.7545 (ttm-80) cc_final: 0.7220 (ttp80) REVERT: B 456 GLU cc_start: 0.7390 (tp30) cc_final: 0.7071 (tp30) REVERT: B 461 GLU cc_start: 0.7666 (tt0) cc_final: 0.7394 (tt0) REVERT: B 469 GLN cc_start: 0.7306 (mt0) cc_final: 0.6988 (tm-30) REVERT: B 481 ARG cc_start: 0.6854 (ttt90) cc_final: 0.6442 (ttp80) REVERT: B 485 GLU cc_start: 0.7125 (tp30) cc_final: 0.6678 (tp30) REVERT: B 498 ASN cc_start: 0.7199 (t0) cc_final: 0.6881 (t0) REVERT: B 517 LYS cc_start: 0.6995 (tppp) cc_final: 0.6698 (tttm) REVERT: B 547 ARG cc_start: 0.6816 (mmm-85) cc_final: 0.6591 (tpp-160) REVERT: C 2 ILE cc_start: 0.8429 (mm) cc_final: 0.8217 (mp) REVERT: C 271 GLU cc_start: 0.6768 (mm-30) cc_final: 0.6550 (tp30) REVERT: C 375 GLU cc_start: 0.7780 (tt0) cc_final: 0.7573 (mt-10) REVERT: C 408 ARG cc_start: 0.7751 (ttm170) cc_final: 0.7435 (ttt-90) REVERT: C 485 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6285 (mm-30) REVERT: D 54 TYR cc_start: 0.8427 (p90) cc_final: 0.8018 (p90) REVERT: D 230 GLU cc_start: 0.6954 (mt-10) cc_final: 0.6734 (mp0) REVERT: D 280 ARG cc_start: 0.6935 (ttt180) cc_final: 0.6617 (ttp80) REVERT: D 394 LYS cc_start: 0.7392 (mttt) cc_final: 0.7029 (mmtt) REVERT: D 466 LYS cc_start: 0.6940 (tttp) cc_final: 0.6664 (tptt) REVERT: E 41 ARG cc_start: 0.6876 (mtp-110) cc_final: 0.6604 (mtp-110) REVERT: E 109 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6941 (tm-30) REVERT: E 216 ARG cc_start: 0.7585 (mtm-85) cc_final: 0.7150 (ptp90) REVERT: E 319 ASP cc_start: 0.7875 (m-30) cc_final: 0.7674 (m-30) REVERT: E 448 GLN cc_start: 0.7115 (tt0) cc_final: 0.6902 (tt0) REVERT: E 453 ARG cc_start: 0.6041 (mmt90) cc_final: 0.5666 (mtt90) REVERT: F 6 LYS cc_start: 0.7177 (tttt) cc_final: 0.6695 (tttp) REVERT: F 72 SER cc_start: 0.8895 (p) cc_final: 0.8541 (p) REVERT: F 251 TYR cc_start: 0.8364 (m-80) cc_final: 0.7891 (m-80) REVERT: F 280 ARG cc_start: 0.6714 (mtm180) cc_final: 0.6488 (mtp180) REVERT: F 376 LYS cc_start: 0.7787 (tptp) cc_final: 0.7484 (tttm) REVERT: F 463 TYR cc_start: 0.8483 (t80) cc_final: 0.8280 (t80) REVERT: G 128 ARG cc_start: 0.4854 (mtp180) cc_final: 0.4513 (mtp85) REVERT: G 148 LYS cc_start: 0.6538 (mttp) cc_final: 0.6274 (mmtm) REVERT: G 184 GLU cc_start: 0.7096 (tt0) cc_final: 0.6862 (mm-30) REVERT: H 14 ARG cc_start: 0.5662 (mtm110) cc_final: 0.4866 (mmm-85) REVERT: H 34 GLU cc_start: 0.5420 (mt-10) cc_final: 0.4880 (mm-30) REVERT: H 49 GLU cc_start: 0.3405 (tm-30) cc_final: 0.2956 (tp30) REVERT: I 104 MET cc_start: 0.5917 (mmp) cc_final: 0.5517 (ttp) REVERT: J 81 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6901 (mm-30) REVERT: J 84 ARG cc_start: 0.4668 (ttt180) cc_final: 0.4409 (ttt90) REVERT: J 86 ARG cc_start: 0.5330 (mtt-85) cc_final: 0.4944 (mmm160) REVERT: J 88 ARG cc_start: 0.6302 (ttm-80) cc_final: 0.5814 (ttp-170) REVERT: J 109 LEU cc_start: 0.5486 (mm) cc_final: 0.5229 (mt) REVERT: K 104 MET cc_start: 0.5283 (mmp) cc_final: 0.4623 (ttp) REVERT: K 106 ARG cc_start: 0.4880 (mmp80) cc_final: 0.3416 (ttm110) REVERT: L 81 GLU cc_start: 0.6090 (tp30) cc_final: 0.5790 (tm-30) REVERT: L 106 LYS cc_start: 0.6463 (ptpt) cc_final: 0.5984 (mmtp) REVERT: L 112 LEU cc_start: 0.5794 (mt) cc_final: 0.5582 (mt) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.2507 time to fit residues: 230.4410 Evaluate side-chains 352 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 HIS B 423 ASN C 316 GLN C 477 GLN E 310 GLN E 364 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 181 GLN ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 130 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.130053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107969 restraints weight = 47048.467| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.59 r_work: 0.3208 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30068 Z= 0.118 Angle : 0.532 7.877 40740 Z= 0.273 Chirality : 0.043 0.142 4567 Planarity : 0.004 0.045 5329 Dihedral : 4.753 102.460 4192 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.88 % Allowed : 6.72 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.14), residues: 3761 helix: 1.94 (0.14), residues: 1531 sheet: -0.20 (0.22), residues: 562 loop : 0.07 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 416 TYR 0.013 0.001 TYR D 331 PHE 0.024 0.001 PHE H 81 TRP 0.012 0.001 TRP B 119 HIS 0.004 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (30067) covalent geometry : angle 0.53179 / 0.27 (40740) hydrogen bonds : bond 0.04933 / 3.31 ( 1291) hydrogen bonds : angle 4.72219 / 3.29 ( 3705) Misc. bond : bond 0.00062 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 414 time to evaluate : 1.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4601 (mtt) cc_final: 0.3864 (ptm) REVERT: A 29 LYS cc_start: 0.8253 (mmtp) cc_final: 0.7923 (mmtt) REVERT: A 54 ASP cc_start: 0.7845 (t0) cc_final: 0.7526 (t70) REVERT: A 98 THR cc_start: 0.8042 (m) cc_final: 0.7515 (p) REVERT: A 159 GLU cc_start: 0.6975 (pp20) cc_final: 0.6605 (pp20) REVERT: A 241 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7892 (mp) REVERT: A 369 ILE cc_start: 0.8607 (mm) cc_final: 0.8365 (mm) REVERT: A 390 ASP cc_start: 0.8074 (t0) cc_final: 0.7789 (t70) REVERT: A 441 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7421 (tt0) REVERT: A 532 ARG cc_start: 0.6627 (mtm-85) cc_final: 0.6264 (ttp80) REVERT: A 550 ARG cc_start: 0.6917 (tpp-160) cc_final: 0.6658 (mmt180) REVERT: A 565 GLU cc_start: 0.6830 (mm-30) cc_final: 0.6380 (pt0) REVERT: A 568 LYS cc_start: 0.7017 (mtmt) cc_final: 0.6708 (tttt) REVERT: B 143 PHE cc_start: 0.6021 (t80) cc_final: 0.5547 (m-80) REVERT: B 156 ARG cc_start: 0.7078 (ptm160) cc_final: 0.6391 (ptp90) REVERT: B 338 SER cc_start: 0.8717 (t) cc_final: 0.8265 (m) REVERT: B 342 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7855 (mt-10) REVERT: B 408 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7856 (ttp80) REVERT: B 461 GLU cc_start: 0.7795 (tt0) cc_final: 0.7503 (tt0) REVERT: B 469 GLN cc_start: 0.7668 (mt0) cc_final: 0.7375 (tm-30) REVERT: B 485 GLU cc_start: 0.7529 (tp30) cc_final: 0.7038 (tp30) REVERT: B 547 ARG cc_start: 0.7308 (mmm-85) cc_final: 0.7036 (tpp-160) REVERT: C 8 LYS cc_start: 0.8897 (tttt) cc_final: 0.8646 (tttm) REVERT: C 130 ARG cc_start: 0.7120 (mtt90) cc_final: 0.6871 (ttm-80) REVERT: C 271 GLU cc_start: 0.6996 (mm-30) cc_final: 0.6787 (tp30) REVERT: D 230 GLU cc_start: 0.7537 (mt-10) cc_final: 0.7295 (mp0) REVERT: D 394 LYS cc_start: 0.7807 (mttt) cc_final: 0.7575 (mmtt) REVERT: E 412 LEU cc_start: 0.8166 (tp) cc_final: 0.7829 (tt) REVERT: E 453 ARG cc_start: 0.6341 (mmt90) cc_final: 0.6102 (mtt90) REVERT: F 6 LYS cc_start: 0.7418 (tttt) cc_final: 0.7183 (tttp) REVERT: G 128 ARG cc_start: 0.4962 (mtp180) cc_final: 0.4600 (mtp85) REVERT: G 148 LYS cc_start: 0.7348 (mttp) cc_final: 0.6983 (mmtm) REVERT: H 14 ARG cc_start: 0.5698 (mtm110) cc_final: 0.4964 (mmm-85) REVERT: H 34 GLU cc_start: 0.5493 (mt-10) cc_final: 0.5118 (mm-30) REVERT: H 49 GLU cc_start: 0.3881 (tm-30) cc_final: 0.3280 (tp30) REVERT: H 59 VAL cc_start: 0.6054 (m) cc_final: 0.5814 (p) REVERT: H 60 GLU cc_start: 0.5759 (mm-30) cc_final: 0.5538 (mm-30) REVERT: H 87 GLU cc_start: 0.6633 (mm-30) cc_final: 0.6309 (tm-30) REVERT: I 104 MET cc_start: 0.5972 (mmp) cc_final: 0.5653 (ttp) REVERT: J 74 GLN cc_start: 0.7237 (tp40) cc_final: 0.6893 (tt0) REVERT: J 81 GLU cc_start: 0.7606 (tm-30) cc_final: 0.7313 (mm-30) REVERT: J 84 ARG cc_start: 0.5403 (ttt180) cc_final: 0.5054 (ttt-90) REVERT: J 88 ARG cc_start: 0.6375 (ttm-80) cc_final: 0.6123 (ttp-170) REVERT: J 109 LEU cc_start: 0.5685 (mm) cc_final: 0.5412 (mt) REVERT: K 104 MET cc_start: 0.5310 (mmp) cc_final: 0.4606 (ttp) REVERT: K 106 ARG cc_start: 0.4915 (mmp80) cc_final: 0.3544 (ttm110) REVERT: L 106 LYS cc_start: 0.6678 (ptpt) cc_final: 0.5991 (mmtp) outliers start: 27 outliers final: 18 residues processed: 433 average time/residue: 0.2449 time to fit residues: 157.8577 Evaluate side-chains 351 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 332 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 489 ILE Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain B residue 530 ILE Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain G residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 199 optimal weight: 7.9990 chunk 160 optimal weight: 10.0000 chunk 313 optimal weight: 8.9990 chunk 143 optimal weight: 2.9990 chunk 138 optimal weight: 9.9990 chunk 265 optimal weight: 4.9990 chunk 315 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 164 optimal weight: 10.0000 chunk 197 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 498 ASN C 316 GLN ** C 418 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 ASN E 310 GLN E 448 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102343 restraints weight = 47787.554| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.66 r_work: 0.3123 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 30068 Z= 0.284 Angle : 0.705 8.695 40740 Z= 0.361 Chirality : 0.050 0.206 4567 Planarity : 0.007 0.071 5329 Dihedral : 5.290 85.658 4192 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.75 % Allowed : 11.13 % Favored : 87.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.13), residues: 3761 helix: 1.23 (0.13), residues: 1561 sheet: -0.43 (0.22), residues: 568 loop : -0.42 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 280 TYR 0.022 0.003 TYR F 331 PHE 0.022 0.003 PHE D 418 TRP 0.013 0.002 TRP C 119 HIS 0.008 0.002 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.28 (30067) covalent geometry : angle 0.70502 / 0.36 (40740) hydrogen bonds : bond 0.06433 / 4.33 ( 1291) hydrogen bonds : angle 4.98133 / 3.46 ( 3705) Misc. bond : bond 0.00085 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 333 time to evaluate : 1.173 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4474 (mtt) cc_final: 0.3599 (ptm) REVERT: A 20 LEU cc_start: 0.7597 (tp) cc_final: 0.7360 (tp) REVERT: A 54 ASP cc_start: 0.8181 (t0) cc_final: 0.7931 (t0) REVERT: A 98 THR cc_start: 0.8051 (m) cc_final: 0.7624 (p) REVERT: A 241 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7983 (mp) REVERT: A 550 ARG cc_start: 0.7040 (tpp-160) cc_final: 0.6819 (mmt180) REVERT: A 568 LYS cc_start: 0.7180 (mtmt) cc_final: 0.6830 (tttt) REVERT: B 143 PHE cc_start: 0.6412 (t80) cc_final: 0.6032 (m-80) REVERT: B 156 ARG cc_start: 0.7193 (ptm160) cc_final: 0.6500 (ptp90) REVERT: B 209 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7805 (mtm) REVERT: B 338 SER cc_start: 0.8919 (t) cc_final: 0.8504 (m) REVERT: B 342 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7909 (mt-10) REVERT: B 408 ARG cc_start: 0.8301 (ttm-80) cc_final: 0.8026 (ttp80) REVERT: B 410 ASP cc_start: 0.7280 (t0) cc_final: 0.7059 (t0) REVERT: B 469 GLN cc_start: 0.7835 (mt0) cc_final: 0.7427 (pp30) REVERT: B 481 ARG cc_start: 0.7878 (ttt90) cc_final: 0.7650 (ttp80) REVERT: B 482 LEU cc_start: 0.8144 (tp) cc_final: 0.7919 (tt) REVERT: B 547 ARG cc_start: 0.7643 (mmm-85) cc_final: 0.7433 (tpp-160) REVERT: C 45 ASP cc_start: 0.8255 (p0) cc_final: 0.8054 (t0) REVERT: C 130 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6751 (ttm-80) REVERT: C 271 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6936 (tp30) REVERT: C 485 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7043 (mm-30) REVERT: D 183 LYS cc_start: 0.6250 (ttmt) cc_final: 0.5996 (ttmm) REVERT: D 394 LYS cc_start: 0.8116 (mttt) cc_final: 0.7828 (mmtt) REVERT: E 41 ARG cc_start: 0.7477 (mtp-110) cc_final: 0.7223 (mtp-110) REVERT: E 61 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7107 (mt-10) REVERT: E 311 ILE cc_start: 0.8704 (pt) cc_final: 0.8489 (mt) REVERT: F 6 LYS cc_start: 0.7733 (tttt) cc_final: 0.7485 (tttp) REVERT: F 376 LYS cc_start: 0.8528 (tptp) cc_final: 0.8266 (tttm) REVERT: G 148 LYS cc_start: 0.7628 (mttp) cc_final: 0.7209 (mmtm) REVERT: H 14 ARG cc_start: 0.5976 (mtm110) cc_final: 0.5164 (mmm-85) REVERT: H 34 GLU cc_start: 0.5532 (mt-10) cc_final: 0.5238 (mm-30) REVERT: H 49 GLU cc_start: 0.4028 (tm-30) cc_final: 0.3404 (tp30) REVERT: I 104 MET cc_start: 0.6003 (mmp) cc_final: 0.5642 (ttp) REVERT: J 74 GLN cc_start: 0.7376 (tp40) cc_final: 0.6910 (tt0) REVERT: J 81 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7282 (mm-30) REVERT: J 109 LEU cc_start: 0.5821 (mm) cc_final: 0.5477 (mt) REVERT: J 119 LYS cc_start: 0.6554 (tptp) cc_final: 0.5982 (ptmt) REVERT: K 104 MET cc_start: 0.5548 (mmp) cc_final: 0.4827 (ttp) REVERT: K 106 ARG cc_start: 0.4943 (mmp80) cc_final: 0.3375 (ttm-80) REVERT: L 106 LYS cc_start: 0.6853 (ptpt) cc_final: 0.6160 (mmtp) outliers start: 54 outliers final: 34 residues processed: 371 average time/residue: 0.2361 time to fit residues: 131.8128 Evaluate side-chains 338 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 302 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 209 MET Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 316 GLN Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 11 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 312 optimal weight: 4.9990 chunk 309 optimal weight: 9.9990 chunk 294 optimal weight: 5.9990 chunk 123 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 8.9990 chunk 208 optimal weight: 9.9990 chunk 279 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 541 GLN C 316 GLN C 418 HIS E 364 ASN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.127495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.106484 restraints weight = 47134.107| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.51 r_work: 0.3185 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30068 Z= 0.145 Angle : 0.536 6.854 40740 Z= 0.274 Chirality : 0.044 0.169 4567 Planarity : 0.005 0.047 5329 Dihedral : 4.863 85.064 4192 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.82 % Allowed : 12.72 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.14), residues: 3761 helix: 1.50 (0.13), residues: 1543 sheet: -0.49 (0.22), residues: 543 loop : -0.34 (0.15), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 50 TYR 0.012 0.001 TYR C 428 PHE 0.020 0.001 PHE H 81 TRP 0.017 0.001 TRP A 119 HIS 0.004 0.001 HIS B 145 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (30067) covalent geometry : angle 0.53584 / 0.27 (40740) hydrogen bonds : bond 0.05005 / 3.37 ( 1291) hydrogen bonds : angle 4.65148 / 3.22 ( 3705) Misc. bond : bond 0.00064 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 324 time to evaluate : 1.250 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4328 (mtt) cc_final: 0.3562 (ptm) REVERT: A 45 ASP cc_start: 0.8326 (OUTLIER) cc_final: 0.8090 (t0) REVERT: A 54 ASP cc_start: 0.8041 (t0) cc_final: 0.7772 (t70) REVERT: A 98 THR cc_start: 0.8041 (m) cc_final: 0.7597 (p) REVERT: A 241 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7877 (mp) REVERT: A 568 LYS cc_start: 0.7050 (mtmt) cc_final: 0.6709 (tttt) REVERT: B 143 PHE cc_start: 0.6278 (t80) cc_final: 0.6029 (m-80) REVERT: B 156 ARG cc_start: 0.7202 (ptm160) cc_final: 0.6450 (ptp90) REVERT: B 338 SER cc_start: 0.8856 (t) cc_final: 0.8395 (m) REVERT: B 342 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7877 (mt-10) REVERT: B 408 ARG cc_start: 0.8137 (ttm-80) cc_final: 0.7860 (ttp80) REVERT: B 410 ASP cc_start: 0.7253 (t0) cc_final: 0.7045 (t0) REVERT: B 469 GLN cc_start: 0.7729 (mt0) cc_final: 0.7345 (pp30) REVERT: B 547 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.7339 (tpp-160) REVERT: C 45 ASP cc_start: 0.8215 (p0) cc_final: 0.7978 (t0) REVERT: C 130 ARG cc_start: 0.7027 (mtt90) cc_final: 0.6658 (ttm-80) REVERT: C 271 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6826 (tp30) REVERT: C 485 GLU cc_start: 0.7304 (mm-30) cc_final: 0.7012 (mm-30) REVERT: C 524 LYS cc_start: 0.8110 (tttm) cc_final: 0.7856 (ttmt) REVERT: D 230 GLU cc_start: 0.8218 (mp0) cc_final: 0.7834 (mp0) REVERT: D 368 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6390 (ptmt) REVERT: D 394 LYS cc_start: 0.7841 (mttt) cc_final: 0.7533 (mmtt) REVERT: E 41 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.7172 (mtp-110) REVERT: E 311 ILE cc_start: 0.8629 (pt) cc_final: 0.8393 (mt) REVERT: F 6 LYS cc_start: 0.7690 (tttt) cc_final: 0.7407 (tttp) REVERT: F 334 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7744 (mm-30) REVERT: G 51 LYS cc_start: 0.6405 (OUTLIER) cc_final: 0.5787 (mmtm) REVERT: G 148 LYS cc_start: 0.7390 (mttp) cc_final: 0.7009 (mmtm) REVERT: H 14 ARG cc_start: 0.5905 (mtm110) cc_final: 0.5144 (mmm-85) REVERT: H 34 GLU cc_start: 0.5600 (mt-10) cc_final: 0.5296 (mm-30) REVERT: H 49 GLU cc_start: 0.3980 (tm-30) cc_final: 0.3336 (tp30) REVERT: H 87 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6131 (mm-30) REVERT: I 87 ARG cc_start: 0.5873 (ptm-80) cc_final: 0.5425 (ptm-80) REVERT: J 74 GLN cc_start: 0.7274 (tp40) cc_final: 0.6918 (tt0) REVERT: J 81 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7265 (mm-30) REVERT: J 109 LEU cc_start: 0.5729 (mm) cc_final: 0.5425 (mt) REVERT: K 104 MET cc_start: 0.5503 (mmp) cc_final: 0.4783 (ttp) REVERT: K 106 ARG cc_start: 0.4902 (mmp80) cc_final: 0.3445 (ttm-80) REVERT: L 106 LYS cc_start: 0.6748 (ptpt) cc_final: 0.6038 (mmtp) outliers start: 56 outliers final: 35 residues processed: 360 average time/residue: 0.2320 time to fit residues: 126.9190 Evaluate side-chains 344 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 303 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain L residue 131 LEU Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 15 optimal weight: 0.0470 chunk 122 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 170 optimal weight: 6.9990 chunk 354 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 253 optimal weight: 0.9990 chunk 322 optimal weight: 0.5980 chunk 208 optimal weight: 7.9990 chunk 278 optimal weight: 5.9990 overall best weight: 2.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107104 restraints weight = 47142.046| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.48 r_work: 0.3201 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 30068 Z= 0.126 Angle : 0.510 6.663 40740 Z= 0.259 Chirality : 0.043 0.198 4567 Planarity : 0.004 0.045 5329 Dihedral : 4.647 78.908 4192 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.14 % Allowed : 13.43 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.14), residues: 3761 helix: 1.67 (0.13), residues: 1546 sheet: -0.46 (0.22), residues: 542 loop : -0.30 (0.15), residues: 1673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 360 TYR 0.012 0.001 TYR C 428 PHE 0.017 0.001 PHE H 81 TRP 0.015 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 (30067) covalent geometry : angle 0.51003 / 0.26 (40740) hydrogen bonds : bond 0.04600 / 3.10 ( 1291) hydrogen bonds : angle 4.50089 / 3.12 ( 3705) Misc. bond : bond 0.00043 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 314 time to evaluate : 1.140 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4327 (mtt) cc_final: 0.3568 (ptm) REVERT: A 54 ASP cc_start: 0.7995 (t0) cc_final: 0.7703 (t70) REVERT: A 97 LYS cc_start: 0.6925 (mtpt) cc_final: 0.6154 (mmtm) REVERT: A 98 THR cc_start: 0.8028 (m) cc_final: 0.7581 (p) REVERT: A 241 LEU cc_start: 0.8188 (OUTLIER) cc_final: 0.7750 (mp) REVERT: A 257 GLU cc_start: 0.7772 (pm20) cc_final: 0.6348 (tt0) REVERT: A 568 LYS cc_start: 0.7013 (mtmt) cc_final: 0.6643 (tttt) REVERT: B 24 MET cc_start: 0.8489 (tpt) cc_final: 0.8194 (tpt) REVERT: B 156 ARG cc_start: 0.7197 (ptm160) cc_final: 0.6726 (ttp-110) REVERT: B 338 SER cc_start: 0.8820 (t) cc_final: 0.8371 (m) REVERT: B 342 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7865 (mt-10) REVERT: B 408 ARG cc_start: 0.8138 (ttm-80) cc_final: 0.7846 (ttp80) REVERT: B 410 ASP cc_start: 0.7279 (t0) cc_final: 0.7062 (t0) REVERT: B 469 GLN cc_start: 0.7710 (mt0) cc_final: 0.7306 (pp30) REVERT: B 547 ARG cc_start: 0.7525 (mmm-85) cc_final: 0.7321 (tpp-160) REVERT: C 8 LYS cc_start: 0.8901 (tttt) cc_final: 0.8575 (tttm) REVERT: C 130 ARG cc_start: 0.7034 (mtt90) cc_final: 0.6653 (ttm-80) REVERT: C 271 GLU cc_start: 0.7228 (mm-30) cc_final: 0.6860 (tp30) REVERT: C 485 GLU cc_start: 0.7325 (mm-30) cc_final: 0.7040 (mm-30) REVERT: C 524 LYS cc_start: 0.8032 (tttm) cc_final: 0.7770 (ttmt) REVERT: D 394 LYS cc_start: 0.7750 (mttt) cc_final: 0.7437 (mmtt) REVERT: E 41 ARG cc_start: 0.7346 (mtp-110) cc_final: 0.7126 (mtp-110) REVERT: F 6 LYS cc_start: 0.7671 (tttt) cc_final: 0.7392 (tttp) REVERT: F 334 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7751 (mm-30) REVERT: F 405 THR cc_start: 0.6496 (OUTLIER) cc_final: 0.6196 (m) REVERT: G 148 LYS cc_start: 0.7368 (mttp) cc_final: 0.6993 (mmtm) REVERT: H 1 MET cc_start: 0.5552 (tpp) cc_final: 0.5238 (ttm) REVERT: H 14 ARG cc_start: 0.5902 (mtm110) cc_final: 0.5133 (mmm-85) REVERT: H 34 GLU cc_start: 0.5598 (mt-10) cc_final: 0.5278 (mm-30) REVERT: H 49 GLU cc_start: 0.3949 (tm-30) cc_final: 0.3314 (tp30) REVERT: H 87 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6057 (mm-30) REVERT: H 89 TYR cc_start: 0.6090 (t80) cc_final: 0.5774 (t80) REVERT: I 87 ARG cc_start: 0.5830 (ptm-80) cc_final: 0.5415 (ptm-80) REVERT: J 74 GLN cc_start: 0.7127 (tp40) cc_final: 0.6817 (tt0) REVERT: J 81 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7333 (mm-30) REVERT: J 109 LEU cc_start: 0.5740 (mm) cc_final: 0.5436 (mt) REVERT: K 104 MET cc_start: 0.5485 (mmp) cc_final: 0.4774 (ttp) REVERT: K 106 ARG cc_start: 0.4785 (mmp80) cc_final: 0.3398 (ttm-80) REVERT: L 106 LYS cc_start: 0.6679 (ptpt) cc_final: 0.6025 (mmtp) outliers start: 66 outliers final: 42 residues processed: 360 average time/residue: 0.2297 time to fit residues: 125.9837 Evaluate side-chains 348 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 302 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 507 CYS Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 362 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 334 GLU Chi-restraints excluded: chain F residue 405 THR Chi-restraints excluded: chain G residue 51 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 355 optimal weight: 7.9990 chunk 271 optimal weight: 8.9990 chunk 351 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 357 optimal weight: 20.0000 chunk 364 optimal weight: 9.9990 chunk 329 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 95 optimal weight: 0.0370 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 overall best weight: 6.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 316 GLN ** F 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.124319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.101763 restraints weight = 47813.010| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.63 r_work: 0.3121 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 30068 Z= 0.290 Angle : 0.690 7.681 40740 Z= 0.353 Chirality : 0.049 0.233 4567 Planarity : 0.006 0.063 5329 Dihedral : 5.260 65.990 4192 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.76 % Allowed : 14.70 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.13), residues: 3761 helix: 1.07 (0.13), residues: 1558 sheet: -0.70 (0.22), residues: 568 loop : -0.65 (0.15), residues: 1635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 360 TYR 0.020 0.002 TYR F 331 PHE 0.025 0.002 PHE G 70 TRP 0.016 0.002 TRP A 119 HIS 0.005 0.002 HIS D 458 Details of bonding type rmsd/Z covalent geometry : bond 0.00712 / 0.29 (30067) covalent geometry : angle 0.69029 / 0.35 (40740) hydrogen bonds : bond 0.06236 / 4.21 ( 1291) hydrogen bonds : angle 4.92720 / 3.42 ( 3705) Misc. bond : bond 0.00114 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 306 time to evaluate : 1.141 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4512 (mtt) cc_final: 0.3723 (ptm) REVERT: A 97 LYS cc_start: 0.7044 (mtpt) cc_final: 0.6257 (mmtm) REVERT: A 98 THR cc_start: 0.8095 (m) cc_final: 0.7671 (p) REVERT: A 241 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7897 (mp) REVERT: A 257 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.6534 (tt0) REVERT: A 262 MET cc_start: 0.7587 (tpp) cc_final: 0.7208 (tpp) REVERT: A 568 LYS cc_start: 0.7184 (mtmt) cc_final: 0.6842 (tttt) REVERT: B 156 ARG cc_start: 0.7236 (ptm160) cc_final: 0.6491 (ptp90) REVERT: B 338 SER cc_start: 0.8935 (t) cc_final: 0.8436 (m) REVERT: B 408 ARG cc_start: 0.8240 (ttm-80) cc_final: 0.7969 (ttp80) REVERT: B 449 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7997 (mt-10) REVERT: B 461 GLU cc_start: 0.7818 (tt0) cc_final: 0.7404 (tt0) REVERT: B 469 GLN cc_start: 0.7781 (mt0) cc_final: 0.7390 (pp30) REVERT: B 493 ASP cc_start: 0.7432 (m-30) cc_final: 0.7216 (m-30) REVERT: B 547 ARG cc_start: 0.7575 (mmm-85) cc_final: 0.7073 (tpp-160) REVERT: B 558 GLU cc_start: 0.5929 (OUTLIER) cc_final: 0.5686 (tp30) REVERT: C 130 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6779 (ttm-80) REVERT: C 271 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7030 (tp30) REVERT: C 485 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7223 (mm-30) REVERT: C 524 LYS cc_start: 0.8251 (tttm) cc_final: 0.7995 (ttmt) REVERT: D 368 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7124 (ptmt) REVERT: D 394 LYS cc_start: 0.8131 (mttt) cc_final: 0.7713 (mmtt) REVERT: E 41 ARG cc_start: 0.7495 (mtp-110) cc_final: 0.7242 (mtp-110) REVERT: E 61 GLU cc_start: 0.7404 (mt-10) cc_final: 0.6999 (mt-10) REVERT: F 6 LYS cc_start: 0.7876 (tttt) cc_final: 0.7534 (tttp) REVERT: F 376 LYS cc_start: 0.8488 (tptp) cc_final: 0.8281 (tttm) REVERT: G 148 LYS cc_start: 0.7664 (mttp) cc_final: 0.7222 (mmtm) REVERT: H 14 ARG cc_start: 0.6007 (mtm110) cc_final: 0.5214 (mmm-85) REVERT: H 34 GLU cc_start: 0.5645 (mt-10) cc_final: 0.5345 (mm-30) REVERT: H 87 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.6239 (mm-30) REVERT: J 81 GLU cc_start: 0.7566 (tm-30) cc_final: 0.7078 (mm-30) REVERT: J 109 LEU cc_start: 0.6008 (mm) cc_final: 0.5636 (mt) REVERT: J 119 LYS cc_start: 0.6480 (tptp) cc_final: 0.6084 (ptmt) REVERT: J 127 ASP cc_start: 0.4152 (OUTLIER) cc_final: 0.3547 (p0) REVERT: K 104 MET cc_start: 0.5505 (mmp) cc_final: 0.4805 (ttp) REVERT: K 106 ARG cc_start: 0.4981 (mmp80) cc_final: 0.3622 (ttp-110) REVERT: L 106 LYS cc_start: 0.6651 (ptpt) cc_final: 0.5933 (mmtp) REVERT: L 109 LEU cc_start: 0.6485 (mt) cc_final: 0.6283 (mt) REVERT: L 141 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.4320 (tm-30) outliers start: 85 outliers final: 60 residues processed: 373 average time/residue: 0.2211 time to fit residues: 127.2989 Evaluate side-chains 354 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 486 VAL Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 156 SER Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 454 ILE Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain J residue 161 THR Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 6 optimal weight: 0.0470 chunk 140 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 215 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 201 optimal weight: 1.9990 chunk 166 optimal weight: 0.9980 chunk 287 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 224 optimal weight: 6.9990 overall best weight: 0.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN C 316 GLN F 425 GLN J 165 ASN L 130 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.128596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105789 restraints weight = 47178.426| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.52 r_work: 0.3183 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 30068 Z= 0.107 Angle : 0.510 7.267 40740 Z= 0.259 Chirality : 0.042 0.214 4567 Planarity : 0.004 0.047 5329 Dihedral : 4.652 69.723 4192 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.88 % Allowed : 15.57 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3761 helix: 1.63 (0.14), residues: 1540 sheet: -0.55 (0.23), residues: 537 loop : -0.38 (0.15), residues: 1684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 360 TYR 0.010 0.001 TYR C 428 PHE 0.018 0.001 PHE H 81 TRP 0.017 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (30067) covalent geometry : angle 0.50975 / 0.26 (40740) hydrogen bonds : bond 0.04452 / 3.00 ( 1291) hydrogen bonds : angle 4.50490 / 3.12 ( 3705) Misc. bond : bond 0.00014 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 312 time to evaluate : 1.151 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4688 (mtt) cc_final: 0.3886 (ptm) REVERT: A 54 ASP cc_start: 0.8095 (t0) cc_final: 0.7786 (t0) REVERT: A 97 LYS cc_start: 0.6949 (mtpt) cc_final: 0.6155 (mmtm) REVERT: A 98 THR cc_start: 0.8031 (m) cc_final: 0.7617 (p) REVERT: A 257 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.6420 (tt0) REVERT: A 555 SER cc_start: 0.7385 (t) cc_final: 0.6853 (p) REVERT: A 568 LYS cc_start: 0.7096 (mtmt) cc_final: 0.6750 (tttt) REVERT: B 24 MET cc_start: 0.8516 (tpt) cc_final: 0.8280 (tpt) REVERT: B 156 ARG cc_start: 0.7275 (ptm160) cc_final: 0.6844 (ttp-110) REVERT: B 338 SER cc_start: 0.8899 (t) cc_final: 0.8438 (m) REVERT: B 342 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7862 (mt-10) REVERT: B 408 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7949 (ttp80) REVERT: B 469 GLN cc_start: 0.7772 (mt0) cc_final: 0.7450 (pp30) REVERT: B 547 ARG cc_start: 0.7505 (mmm-85) cc_final: 0.6949 (tpp-160) REVERT: B 558 GLU cc_start: 0.5866 (OUTLIER) cc_final: 0.5623 (tp30) REVERT: C 8 LYS cc_start: 0.8892 (tttt) cc_final: 0.8599 (tttm) REVERT: C 130 ARG cc_start: 0.7225 (mtt90) cc_final: 0.6772 (ttm-80) REVERT: C 271 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6939 (tp30) REVERT: C 524 LYS cc_start: 0.8125 (tttm) cc_final: 0.7881 (ttmt) REVERT: D 368 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7105 (ptmt) REVERT: D 394 LYS cc_start: 0.7912 (mttt) cc_final: 0.7555 (mmtt) REVERT: F 6 LYS cc_start: 0.7788 (tttt) cc_final: 0.7498 (tttp) REVERT: G 148 LYS cc_start: 0.7567 (mttp) cc_final: 0.7193 (mmtm) REVERT: H 1 MET cc_start: 0.5535 (tpp) cc_final: 0.5279 (ttm) REVERT: H 14 ARG cc_start: 0.5899 (mtm110) cc_final: 0.5135 (mmm-85) REVERT: H 34 GLU cc_start: 0.5570 (mt-10) cc_final: 0.5182 (mm-30) REVERT: H 49 GLU cc_start: 0.3700 (tm-30) cc_final: 0.3082 (tp30) REVERT: H 87 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6185 (mm-30) REVERT: J 74 GLN cc_start: 0.7240 (tp40) cc_final: 0.6910 (tt0) REVERT: J 81 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7216 (mm-30) REVERT: J 109 LEU cc_start: 0.5905 (mm) cc_final: 0.5605 (mt) REVERT: K 104 MET cc_start: 0.5470 (mmp) cc_final: 0.4788 (ttp) REVERT: K 106 ARG cc_start: 0.4888 (mmp80) cc_final: 0.3438 (ttm-80) REVERT: L 106 LYS cc_start: 0.6631 (ptpt) cc_final: 0.5882 (mmtp) outliers start: 58 outliers final: 35 residues processed: 353 average time/residue: 0.2309 time to fit residues: 124.4806 Evaluate side-chains 328 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 289 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 117 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 372 optimal weight: 9.9990 chunk 295 optimal weight: 10.0000 chunk 217 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 264 optimal weight: 8.9990 chunk 289 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN B 541 GLN L 165 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.125338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.102867 restraints weight = 47666.239| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 1.63 r_work: 0.3132 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 30068 Z= 0.247 Angle : 0.640 10.781 40740 Z= 0.326 Chirality : 0.048 0.321 4567 Planarity : 0.006 0.053 5329 Dihedral : 5.049 61.206 4192 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.56 % Allowed : 15.67 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.14), residues: 3761 helix: 1.29 (0.13), residues: 1538 sheet: -0.68 (0.23), residues: 538 loop : -0.64 (0.14), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 360 TYR 0.019 0.002 TYR C 428 PHE 0.018 0.002 PHE G 70 TRP 0.016 0.002 TRP A 119 HIS 0.004 0.001 HIS E 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.25 (30067) covalent geometry : angle 0.63963 / 0.33 (40740) hydrogen bonds : bond 0.05688 / 3.84 ( 1291) hydrogen bonds : angle 4.76430 / 3.31 ( 3705) Misc. bond : bond 0.00090 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 287 time to evaluate : 1.418 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4680 (mtt) cc_final: 0.3895 (ptm) REVERT: A 97 LYS cc_start: 0.7016 (mtpt) cc_final: 0.6234 (mmtm) REVERT: A 98 THR cc_start: 0.8016 (m) cc_final: 0.7594 (p) REVERT: A 241 LEU cc_start: 0.8249 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 257 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6498 (tt0) REVERT: A 555 SER cc_start: 0.7443 (OUTLIER) cc_final: 0.6917 (p) REVERT: A 565 GLU cc_start: 0.6750 (mm-30) cc_final: 0.6443 (mm-30) REVERT: A 568 LYS cc_start: 0.7170 (mtmt) cc_final: 0.6838 (tttt) REVERT: B 156 ARG cc_start: 0.7253 (ptm160) cc_final: 0.6829 (ttp-110) REVERT: B 338 SER cc_start: 0.8944 (t) cc_final: 0.8445 (m) REVERT: B 408 ARG cc_start: 0.8246 (ttm-80) cc_final: 0.7964 (ttp80) REVERT: B 410 ASP cc_start: 0.7604 (t0) cc_final: 0.7395 (t0) REVERT: B 449 GLU cc_start: 0.8257 (mm-30) cc_final: 0.7989 (mt-10) REVERT: B 469 GLN cc_start: 0.7767 (mt0) cc_final: 0.7388 (pp30) REVERT: B 547 ARG cc_start: 0.7559 (mmm-85) cc_final: 0.7046 (tpp-160) REVERT: B 558 GLU cc_start: 0.5948 (OUTLIER) cc_final: 0.5678 (tp30) REVERT: C 130 ARG cc_start: 0.7149 (mtt90) cc_final: 0.6748 (ttm-80) REVERT: C 271 GLU cc_start: 0.7353 (mm-30) cc_final: 0.7049 (tp30) REVERT: C 524 LYS cc_start: 0.8238 (tttm) cc_final: 0.7987 (ttmt) REVERT: D 368 LYS cc_start: 0.7686 (OUTLIER) cc_final: 0.7124 (ptmt) REVERT: D 394 LYS cc_start: 0.7953 (mttt) cc_final: 0.7610 (mmtt) REVERT: E 318 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6767 (m-30) REVERT: F 6 LYS cc_start: 0.7943 (tttt) cc_final: 0.7584 (tttp) REVERT: G 148 LYS cc_start: 0.7665 (mttp) cc_final: 0.7199 (mmtm) REVERT: H 1 MET cc_start: 0.5760 (tpp) cc_final: 0.5493 (ttm) REVERT: H 14 ARG cc_start: 0.6017 (mtm110) cc_final: 0.5224 (mmm-85) REVERT: H 34 GLU cc_start: 0.5662 (mt-10) cc_final: 0.5303 (mm-30) REVERT: H 47 VAL cc_start: 0.6976 (OUTLIER) cc_final: 0.6485 (p) REVERT: H 87 GLU cc_start: 0.6892 (OUTLIER) cc_final: 0.6207 (mm-30) REVERT: J 74 GLN cc_start: 0.7264 (tp40) cc_final: 0.6888 (tt0) REVERT: J 81 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7111 (mm-30) REVERT: J 109 LEU cc_start: 0.6002 (mm) cc_final: 0.5663 (mt) REVERT: K 104 MET cc_start: 0.5553 (mmp) cc_final: 0.4853 (ttp) REVERT: K 106 ARG cc_start: 0.5081 (mmp80) cc_final: 0.3640 (ttm-80) REVERT: L 106 LYS cc_start: 0.6638 (ptpt) cc_final: 0.5973 (mmtp) REVERT: L 141 GLU cc_start: 0.5539 (OUTLIER) cc_final: 0.4276 (tm-30) outliers start: 79 outliers final: 56 residues processed: 344 average time/residue: 0.2198 time to fit residues: 117.2299 Evaluate side-chains 347 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 282 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain A residue 422 ILE Chi-restraints excluded: chain A residue 457 LEU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 433 SER Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 540 LEU Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 380 ASP Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 36 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain F residue 459 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain J residue 94 LEU Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 62 optimal weight: 8.9990 chunk 145 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 184 optimal weight: 0.8980 chunk 280 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 240 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 316 GLN J 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.128265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.105544 restraints weight = 47134.875| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.51 r_work: 0.3175 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30068 Z= 0.119 Angle : 0.521 10.989 40740 Z= 0.264 Chirality : 0.043 0.283 4567 Planarity : 0.004 0.046 5329 Dihedral : 4.630 60.069 4192 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.85 % Allowed : 16.32 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.14), residues: 3761 helix: 1.61 (0.14), residues: 1541 sheet: -0.61 (0.22), residues: 542 loop : -0.43 (0.15), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 360 TYR 0.011 0.001 TYR C 428 PHE 0.019 0.001 PHE H 81 TRP 0.017 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (30067) covalent geometry : angle 0.52117 / 0.26 (40740) hydrogen bonds : bond 0.04461 / 3.01 ( 1291) hydrogen bonds : angle 4.49374 / 3.12 ( 3705) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 287 time to evaluate : 1.100 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4644 (mtt) cc_final: 0.4131 (ptm) REVERT: A 54 ASP cc_start: 0.8074 (t0) cc_final: 0.7756 (t0) REVERT: A 97 LYS cc_start: 0.6952 (mtpt) cc_final: 0.6168 (mmtm) REVERT: A 98 THR cc_start: 0.7985 (m) cc_final: 0.7568 (p) REVERT: A 257 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6293 (mt-10) REVERT: A 555 SER cc_start: 0.7370 (t) cc_final: 0.6885 (p) REVERT: A 568 LYS cc_start: 0.7097 (mtmt) cc_final: 0.6709 (tttt) REVERT: B 24 MET cc_start: 0.8526 (tpt) cc_final: 0.8290 (tpt) REVERT: B 156 ARG cc_start: 0.7215 (ptm160) cc_final: 0.6825 (ttp-110) REVERT: B 338 SER cc_start: 0.8919 (t) cc_final: 0.8407 (m) REVERT: B 342 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 408 ARG cc_start: 0.8229 (ttm-80) cc_final: 0.7932 (ttp80) REVERT: B 469 GLN cc_start: 0.7672 (mt0) cc_final: 0.7389 (pp30) REVERT: B 547 ARG cc_start: 0.7500 (mmm-85) cc_final: 0.6926 (tpp-160) REVERT: B 558 GLU cc_start: 0.5848 (OUTLIER) cc_final: 0.5584 (tp30) REVERT: C 8 LYS cc_start: 0.8910 (tttt) cc_final: 0.8605 (tttm) REVERT: C 130 ARG cc_start: 0.7095 (mtt90) cc_final: 0.6698 (ttm-80) REVERT: C 271 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6889 (tp30) REVERT: C 524 LYS cc_start: 0.8085 (tttm) cc_final: 0.7872 (ttmt) REVERT: D 349 TYR cc_start: 0.8483 (t80) cc_final: 0.8241 (t80) REVERT: D 368 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7097 (ptmt) REVERT: D 394 LYS cc_start: 0.7911 (mttt) cc_final: 0.7549 (mmtt) REVERT: F 6 LYS cc_start: 0.7817 (tttt) cc_final: 0.7503 (tttp) REVERT: G 148 LYS cc_start: 0.7529 (mttp) cc_final: 0.7149 (mmtm) REVERT: H 14 ARG cc_start: 0.5933 (mtm110) cc_final: 0.5184 (mmm-85) REVERT: H 34 GLU cc_start: 0.5588 (mt-10) cc_final: 0.5189 (mm-30) REVERT: H 47 VAL cc_start: 0.7031 (OUTLIER) cc_final: 0.6530 (p) REVERT: H 87 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6206 (mm-30) REVERT: J 74 GLN cc_start: 0.7239 (tp40) cc_final: 0.6927 (tt0) REVERT: J 81 GLU cc_start: 0.7625 (tm-30) cc_final: 0.7386 (tt0) REVERT: J 109 LEU cc_start: 0.5990 (mm) cc_final: 0.5678 (mt) REVERT: K 104 MET cc_start: 0.5456 (mmp) cc_final: 0.4799 (ttp) REVERT: K 106 ARG cc_start: 0.4848 (mmp80) cc_final: 0.3532 (ttm-80) REVERT: L 106 LYS cc_start: 0.6627 (ptpt) cc_final: 0.5976 (mmtp) outliers start: 57 outliers final: 44 residues processed: 328 average time/residue: 0.2072 time to fit residues: 104.6595 Evaluate side-chains 329 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 280 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 558 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 161 THR Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 370 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 109 optimal weight: 1.9990 chunk 346 optimal weight: 10.0000 chunk 331 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 278 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 366 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 316 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.101834 restraints weight = 47674.284| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.51 r_work: 0.3123 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 30068 Z= 0.282 Angle : 0.691 10.365 40740 Z= 0.352 Chirality : 0.049 0.288 4567 Planarity : 0.006 0.062 5329 Dihedral : 5.246 57.045 4192 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.24 % Allowed : 16.19 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.03 (0.13), residues: 3761 helix: 1.06 (0.13), residues: 1547 sheet: -0.77 (0.22), residues: 568 loop : -0.72 (0.15), residues: 1646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 460 TYR 0.020 0.002 TYR C 428 PHE 0.021 0.002 PHE G 70 TRP 0.013 0.002 TRP A 119 HIS 0.005 0.002 HIS E 375 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.28 (30067) covalent geometry : angle 0.69054 / 0.35 (40740) hydrogen bonds : bond 0.06118 / 4.13 ( 1291) hydrogen bonds : angle 4.88703 / 3.40 ( 3705) Misc. bond : bond 0.00104 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7522 Ramachandran restraints generated. 3761 Oldfield, 0 Emsley, 3761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 288 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4613 (mtt) cc_final: 0.4263 (ptm) REVERT: A 97 LYS cc_start: 0.7092 (mtpt) cc_final: 0.6302 (mmtm) REVERT: A 98 THR cc_start: 0.8039 (m) cc_final: 0.7611 (p) REVERT: A 241 LEU cc_start: 0.8267 (OUTLIER) cc_final: 0.7909 (mp) REVERT: A 257 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6351 (mt-10) REVERT: A 555 SER cc_start: 0.7430 (OUTLIER) cc_final: 0.6974 (p) REVERT: A 565 GLU cc_start: 0.6757 (mm-30) cc_final: 0.6333 (mm-30) REVERT: A 568 LYS cc_start: 0.7192 (mtmt) cc_final: 0.6860 (tttt) REVERT: B 156 ARG cc_start: 0.7090 (ptm160) cc_final: 0.6813 (ttp-110) REVERT: B 338 SER cc_start: 0.8944 (t) cc_final: 0.8439 (m) REVERT: B 408 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7961 (ttp80) REVERT: B 449 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7997 (mt-10) REVERT: B 469 GLN cc_start: 0.7773 (mt0) cc_final: 0.7390 (pp30) REVERT: B 547 ARG cc_start: 0.7690 (mmm-85) cc_final: 0.7231 (tpp-160) REVERT: C 130 ARG cc_start: 0.7094 (mtt90) cc_final: 0.6759 (ttm-80) REVERT: C 271 GLU cc_start: 0.7324 (mm-30) cc_final: 0.7006 (tp30) REVERT: C 524 LYS cc_start: 0.8251 (tttm) cc_final: 0.8005 (ttmt) REVERT: D 368 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7159 (ptmt) REVERT: E 61 GLU cc_start: 0.7415 (mt-10) cc_final: 0.6991 (mt-10) REVERT: E 318 ASP cc_start: 0.7192 (OUTLIER) cc_final: 0.6792 (m-30) REVERT: F 6 LYS cc_start: 0.7981 (tttt) cc_final: 0.7648 (tttp) REVERT: F 376 LYS cc_start: 0.8520 (tptp) cc_final: 0.8306 (tttm) REVERT: G 148 LYS cc_start: 0.7725 (mttp) cc_final: 0.7240 (mmtm) REVERT: H 14 ARG cc_start: 0.6110 (mtm110) cc_final: 0.5346 (mmm-85) REVERT: H 34 GLU cc_start: 0.5685 (mt-10) cc_final: 0.5281 (mm-30) REVERT: H 47 VAL cc_start: 0.6936 (OUTLIER) cc_final: 0.6435 (p) REVERT: H 87 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6338 (mm-30) REVERT: J 74 GLN cc_start: 0.7303 (tp40) cc_final: 0.6899 (tt0) REVERT: J 81 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7277 (tt0) REVERT: J 109 LEU cc_start: 0.6029 (mm) cc_final: 0.5616 (mt) REVERT: J 119 LYS cc_start: 0.6477 (ttpt) cc_final: 0.6013 (ptmt) REVERT: J 127 ASP cc_start: 0.3742 (OUTLIER) cc_final: 0.3126 (p0) REVERT: K 104 MET cc_start: 0.5684 (mmp) cc_final: 0.5206 (mtp) REVERT: K 106 ARG cc_start: 0.5108 (mmp80) cc_final: 0.3617 (ttm-80) REVERT: L 106 LYS cc_start: 0.6470 (ptpt) cc_final: 0.5896 (mmtp) REVERT: L 141 GLU cc_start: 0.5588 (OUTLIER) cc_final: 0.4293 (tm-30) outliers start: 69 outliers final: 48 residues processed: 340 average time/residue: 0.2209 time to fit residues: 116.1027 Evaluate side-chains 336 residues out of total 3082 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 279 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 CYS Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 160 VAL Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 374 GLU Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 555 SER Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 158 LYS Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 326 SER Chi-restraints excluded: chain B residue 390 ASP Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 467 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain D residue 26 ASP Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 368 LYS Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 100 ILE Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 366 VAL Chi-restraints excluded: chain E residue 405 THR Chi-restraints excluded: chain E residue 433 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 72 SER Chi-restraints excluded: chain F residue 88 MET Chi-restraints excluded: chain F residue 290 ASP Chi-restraints excluded: chain G residue 58 LYS Chi-restraints excluded: chain G residue 101 VAL Chi-restraints excluded: chain G residue 143 THR Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 86 VAL Chi-restraints excluded: chain H residue 87 GLU Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain J residue 122 VAL Chi-restraints excluded: chain J residue 127 ASP Chi-restraints excluded: chain L residue 141 GLU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 252 optimal weight: 8.9990 chunk 328 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 138 optimal weight: 0.9980 chunk 322 optimal weight: 9.9990 chunk 87 optimal weight: 0.9990 chunk 344 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 185 optimal weight: 3.9990 chunk 145 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.103946 restraints weight = 47542.109| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.52 r_work: 0.3156 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 30068 Z= 0.162 Angle : 0.571 11.832 40740 Z= 0.289 Chirality : 0.045 0.274 4567 Planarity : 0.005 0.048 5329 Dihedral : 4.876 52.414 4192 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.01 % Allowed : 16.48 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3761 helix: 1.34 (0.13), residues: 1536 sheet: -0.74 (0.23), residues: 537 loop : -0.62 (0.15), residues: 1688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 460 TYR 0.014 0.001 TYR C 428 PHE 0.017 0.001 PHE H 81 TRP 0.017 0.001 TRP A 119 HIS 0.004 0.001 HIS C 418 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.16 (30067) covalent geometry : angle 0.57102 / 0.29 (40740) hydrogen bonds : bond 0.05044 / 3.41 ( 1291) hydrogen bonds : angle 4.65941 / 3.24 ( 3705) Misc. bond : bond 0.00058 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7514.60 seconds wall clock time: 129 minutes 21.02 seconds (7761.02 seconds total)